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- PDB-7al6: Crystal structure of the hypothetical protein PA1622 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 7al6
TitleCrystal structure of the hypothetical protein PA1622 from Pseudomonas aeruginosa PAO1
ComponentsProbable hydrolase
KeywordsUNKNOWN FUNCTION / Pseudomonas aeruginosa / hypothetical protein / Alpha/Beta hydrolase fold / Putative lipolytic enzyme
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Probable hydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFeiler, C.G. / Blankenfeldt, W.
CitationJournal: To Be Published
Title: Crystal structure of the hypothetical protein PA1622 from Pseudomonas aeruginosa PAO1
Authors: Feiler, C.G. / Blankenfeldt, W.
History
DepositionOct 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable hydrolase
B: Probable hydrolase
C: Probable hydrolase
D: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,41615
Polymers125,3374
Non-polymers1,07911
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-47 kcal/mol
Surface area43670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.758, 136.758, 148.126
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Probable hydrolase


Mass: 31334.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA1622 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I3A0
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.24 M magnesium formate 22% PEG 3350 20mg/ml protein concentration

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→44.76 Å / Num. obs: 91339 / % possible obs: 99.97 % / Redundancy: 8.7 % / Biso Wilson estimate: 34.36 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.034 / Rrim(I) all: 0.095 / Net I/σ(I): 15.71
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 9065 / CC1/2: 0.753 / CC star: 0.927 / Rpim(I) all: 0.328 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AL5

7al5


Resolution: 2.1→44.76 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 4540 4.97 %
Rwork0.163 --
obs0.1652 91329 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8778 0 71 666 9515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139101
X-RAY DIFFRACTIONf_angle_d1.46312332
X-RAY DIFFRACTIONf_dihedral_angle_d20.7541290
X-RAY DIFFRACTIONf_chiral_restr0.0661369
X-RAY DIFFRACTIONf_plane_restr0.011604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.27721510.23362844X-RAY DIFFRACTION100
2.12-2.150.28451480.21552902X-RAY DIFFRACTION100
2.15-2.180.24961690.21952851X-RAY DIFFRACTION100
2.18-2.20.27151410.20122896X-RAY DIFFRACTION100
2.2-2.230.20941520.20262876X-RAY DIFFRACTION100
2.23-2.260.26721210.18942891X-RAY DIFFRACTION100
2.26-2.290.24221420.1842922X-RAY DIFFRACTION100
2.29-2.330.23491360.17912925X-RAY DIFFRACTION100
2.33-2.370.21611510.17862877X-RAY DIFFRACTION100
2.37-2.40.2071460.17222889X-RAY DIFFRACTION100
2.4-2.450.24031600.17182892X-RAY DIFFRACTION100
2.45-2.490.22421490.1752906X-RAY DIFFRACTION100
2.49-2.540.24471430.17212870X-RAY DIFFRACTION100
2.54-2.590.25591440.16712897X-RAY DIFFRACTION100
2.59-2.650.22331220.17622909X-RAY DIFFRACTION100
2.65-2.710.24091490.17742880X-RAY DIFFRACTION100
2.71-2.770.21321650.17072883X-RAY DIFFRACTION100
2.78-2.850.21191750.16662911X-RAY DIFFRACTION100
2.85-2.930.20961700.16822825X-RAY DIFFRACTION100
2.93-3.030.20961450.17632919X-RAY DIFFRACTION100
3.03-3.140.23881750.16762862X-RAY DIFFRACTION100
3.14-3.260.23761530.17892899X-RAY DIFFRACTION100
3.26-3.410.23721610.17112908X-RAY DIFFRACTION100
3.41-3.590.22851610.15762874X-RAY DIFFRACTION100
3.59-3.820.17211460.14672904X-RAY DIFFRACTION100
3.82-4.110.16411250.13592938X-RAY DIFFRACTION100
4.11-4.520.16861540.12682877X-RAY DIFFRACTION100
4.52-5.180.15421720.12982905X-RAY DIFFRACTION100
5.18-6.520.22761390.16482946X-RAY DIFFRACTION100
6.52-44.760.17621750.17032911X-RAY DIFFRACTION100

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